CombeChem e-Science at the American Chemical Society Meeting (ACS) 2005
Sunday 13th to Thursday 17th March 2005
Held in San Diego, California
The ACS meeting runs a symposium on Chemical Information (CINF). CombeChem and e-Bank were represented in a series of talks in the High Throughput Informatics and the General Informatics Sections with talks from Jeremy Frey, Jon Essex and Simon Coles. Simon's Poster was also selected for the SCI MIX session.
Triple store databases and their role in high throughput, automated, extensible data analysis
Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, and Jeremy G. Frey
Informatics and High Throughput Experimentation Session
A critical component of high throughput experiments is the ability to store, retrieve, and analyse the resulting data. This is arguably best accomplished using a relational database. However, an elaborate relational database is founded on a complicated schema, and changing this schema requires a major act of redesign. This is incompatible with the scientific method, however, by which new hypotheses are devised and tested. Triple store databases, on the other hand, are able to be modified and extended without requiring a major redesign. In this presentation, the triple store method, and its application to the cheminformatics problem of solubility prediction, will be described.
San Diego the home of
the Smart Corner
Semantic support for smart laboratories
Jeremy G. Frey, Hugo R. Mills, Gareth V. Hughes, Jamie Robinson, Dave De Roure, monica m.c. schraefel, and Luc Moreau
The electronic notebook is an integral part of a smart laboratory and is one of the main ways the laboratory record is generated. Triple stores containing RDF and other semantically-rich information provide a basis for recording this information in a flexible manner, and ultimately to allow automated semantic reasoning on the stored information. These automatic processes are essential not only for subsequent analysis but also to provide suitable context with which to place observations in their proper place in the experiment record, and to ensure that the electronic lab book adjusts itself to the context in which it is being used. Information flows from other sources, such as environmental monitors for temperature and humidity, or systems from tracking researchers' presence, contribute to and annotate the records generated as the experiments are run and are conveniently handled using middleware tools including data broker services. Examples of how these systems have been set up and the way they aid chemical investigations.
Jon Essex presented a talk on the BioSimGrid project
BioSimGrid: A distributed database for the storage and analysis of biomolecular computer simulations
Jonathan W. Essex, Stuart E. Murdock, Robert J. Gledhill, Kaihsu Tai, Muan Hong Ng, Steve Johnston, Bing Wu, Hans Fangohr, Paul Jeffreys, Simon Cox, and Mark Sansom
BioSimGrid aims to deliver a biomolecular simulation data repository to enable more efficient storage, access, exchange and analysis of biomolecular simulation data. The project seeks to exploit the concepts of the Grid, where large computational and data resources are made available to users in a highly accessible manner. The ability to submit, search, query, retrieve, and post-process biomolecular simulation data in a uniform way is important for allowing more efficient data sharing. In this presentation, the design and operation of the current version of the software will be described, and future extensions outlined. The application of BioSimGrid to the comparative analysis of a number of protein simulations (acetylcholinesterase with bacterial outer-membrane phospholipase, and a number of mutants of the prion protein with each other) will also be presented.
Simon Coles presented a poster and a talk on the Crystal Grid, e-Bank and Combechem Agenda
Data publication @ source via the open archive initiative Sci-Mix Poster
Simon J. Coles, Jeremy G Frey, Michael B. Hursthouse, Leslie A Carr, and Christopher J Gutteridge
A crystallography-based exemplar for open archive publication of scientific data will be presented.
Advances in instrumentation and computation have caused an explosion of scientific data. However, this has not resulted in the expected growth of scientific databases and the reason for this can be clearly identified as a publication bottleneck. As a result of this situation, the user community is deprived of valuable information, and the funding bodies are getting a poor return for their investments!
The RDF Matrix - the semantic
underpinning of the CombeChem
Unlike other disciplines the chemical sciences have been reluctant or slow to embrace the 'preprint concept'. This poster outlines a pre-print procedure for the rapid and effective dissemination of structural information to the scientific community (eCrystals) which removes the lengthy peer review process that hampers traditional publication routes, but provides an alternative mechanism. eCrystals is built on a concept developed in the computer science community whereby an author may reveal archives of information to the public. eCrystals makes available all raw, derived and results data from a crystallographic experiment via a searchable and hierarchical system. Bibliographic and chemical metadata items, which are associated with the data, are published through standard protocols and therefore immediately and globally disseminated.
Hence scientific data may be disseminated in a manner that anyone wishing to utilise the information may access the entire archive of data related to it and assess its validity and worth. Recent advances in developing this approach to openly publish ANY form of chemical, or indeed scientific, data will also be presented.
How "crystalloinformatics" can enable chemoinformatics
Simom J. Coles
Recent work by the UK National Crystallography Service (NCS) (http://www.soton.ac.uk/~xservice) has been aimed at developing an eScience infrastructure to facilitate the end-to-end crystallographic experiment. In addition to this recent advances in instrumentation and computational resources have dramatically increased the output of the crystallographic laboratory. However this presents a new problem in the dissemination of these vast amounts of structural data and information through current peer review publication protocols. Thus the funding bodies are getting poor value for money in their investments and the chemistry and chemoinformatics communities are being deprived of valuable data. The eBank-UK project (http://www.ukoln.ac.uk/projects/ebank-uk/) addresses the issue of dissemination of scientific data and uses the philosophy of the Open Archive Initiative (OAI) to solve this problem.
The NCS has developed an Open Access Archive of crystal structure data (http://ecrystals.chem.soton.ac.uk) which is operated in a similar fashion to an institutional repository. All the data generated during the course of the crystal structure experiment is deposited in an OAA with attached metadata, such as chemical name, empirical formula, authors, institution, International Chemical Identifier (INChI), etc. These metadata are exported to the public domain through the OAI Protocol for Metadata Harvesting (OAI-PMH) following conventional protocols for open publication (Dublin Core). This methodology allows electronic harvesting agents to visit the archive and gather any new metadata, which may then be stored, aggregated and linked by information provision services. The OAI publishing of crystallography data not only allows a fast track route to the public for reuse of this data, but it also enables more detailed discussions of chemistry in conventional journal publications without the distracting reproduction of experimental data. The informatician may easily discover the existence of structural chemistry data, seamlessly navigate to any aspect of it, openly access it and download it for reuse in a further 'value added' studies.
Link to Simon's Talk http://eprints.soton.ac.uk/15162/
Jon Essex also gave a simulation talk in the Division of Computers in Chemistry (COMP) on his simulation work
Application of digital filters to enhance conformational change in protein systems
Adrian P. Wiley and Jonathan W Essex
ACS Abstract: http://oasys2.confex.com/acs/229nm/techprogram/P833231.HTM
Motions in biological molecules can occur on timescales beyond those accessible to molecular dynamics simulations, and algorithms that enhance conformational sampling are therefore of considerable interest. Reversible Digitally Filtered Molecular Dynamics (RDFMD) is able to enhance sampling by amplifying the low frequency motions as a simulation evolves. In this presentation, methods to optimise the performance of RDFMD are described, and applications of this approach to enhancing the conformational motion in E. coli dihydrofolate reductase, T4 lysozyme, and HIV-1 protease, are described.
Next ACS Meetings
230th - Washington, DC
August 28 - September 1,
231st - Atlanta, GA
March 26 - 30, 2006
232nd - San Francisco, CA
September 10 - 14, 2006
233rd - Chicago, IL
March 25 - 29, 2007